The city of Rithymno already existed from the Late Minoan Period III as at the settlement of Mastaba a Minoan cemetery of Ancient Rithymnas was found in 1947. Archaeological excavation discovered mosaics of the Roman and Byzantine age. But also during the 3 century A.D. the city seems to have acquired great significance as it was referred to a large village by Claudius Amiliano.
During the first Byzantine period the city is inhabited and the most important cities were Lappa and Eleftherna as the Sees of bishops.
During the period of Venetian rule, Rethymno begins to become a city, with its conquerors taking advantage of its geographical position and building the port which still survives, the Mandraki. Rethymno underwent many disaster from pirate (1538), raiders who (1567) pillage, rob and set it on fire. Later in 1590, a terrible flood was catastrophic for the island.
The Turks occupied the city afterwards after a 22 day siege in November of 1646. During the period of Turkish rule of Rethymno it followed the fortune of the other cities and many martyr heroes were distinguished in the struggle against the conqueror and who are commemorated.